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Clec16a, Nrdp1, and USP8 Form a Ubiquitin-Dependent

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Clec16a, Nrdp1, and USP8 Form a Ubiquitin-Dependent Page 1 of 46 Diabetes Clec16a, Nrdp1, and USP8 form a ubiquitin-dependent tripartite complex that regulates beta cell mitophagy Gemma Pearson1; Biaoxin Chai1; Tracy Vozheiko1; Xueying Liu1; Malathi Kandarpa2; 3 1,4* Robert C. Piper ; and Scott A. Soleimanpour 1Division of Metabolism, Endocrinology & Diabetes, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48105, USA. 2Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48105, USA. 3Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA 4Veterans Affairs Ann Arbor Health Care System, Ann Arbor, MI 48105, USA. *Corresponding Author Scott A. Soleimanpour, M.D., 1000 Wall Street, 5317 Brehm Tower, Ann Arbor, MI 48105. Phone: (734) 763-0528 Fax: (734) 232-8162 E-mail: [email protected] Running Title: β-cell mitophagy requires ubiquitin signaling Word Count: 4448 Figures: 7 Diabetes Publish Ahead of Print, published online November 27, 2017 Diabetes Page 2 of 46 ABSTRACT Mitophagy is a cellular quality control pathway, which is essential to eliminate unhealthy mitochondria. While mitophagy is critical to pancreatic β-cell function, the post-translational signals governing β-cell mitochondrial turnover are unknown. Here we report that ubiquitination is essential for the assembly of a mitophagy regulatory complex, comprised of the E3 ligase Nrdp1, the deubiquitinase enzyme USP8, and Clec16a, a mediator of β-cell mitophagy with unclear function. We discover that the diabetes gene Clec16a encodes an E3 ligase, which promotes non-degradative ubiquitin conjugates to direct its mitophagy effectors and stabilize the Clec16a-Nrdp1-USP8 complex. Inhibition of the Clec16a pathway by the chemotherapeutic lenalidomide, a selective ubiquitin ligase inhibitor associated with new onset diabetes, impairs β-cell mitophagy, oxygen consumption, and insulin secretion. Indeed, patients treated with lenalidomide develop compromised β-cell function. Moreover, the β-cell Clec16a-Nrdp1-USP8 mitophagy complex is destabilized and dysfunctional following lenalidomide treatment as well as following glucolipotoxic stress. Thus, the Clec16a-Nrdp1- USP8 complex relies on ubiquitin signals to promote mitophagy and maintain mitochondrial quality control necessary for optimal β-cell function. 2 Page 3 of 46 Diabetes Pancreatic β-cells rely on mitochondrial bioenergetics to fuel glucose-stimulated insulin secretion (GSIS), which is essential for normal glucose homeostasis and is impaired in all forms of diabetes (1). Beyond respiratory function, the mass of healthy mitochondria, regulated by a balance of mitochondrial biogenesis and turnover, is vital to maintain energy demands for proper stimulus-secretion coupling. Mitochondrial autophagy (mitophagy) is a quality control mechanism necessary for the selective elimination of dysfunctional mitochondria to maintain optimal mitochondrial respiration in many cell types, including β- cells (2; 3). Despite the importance of mitophagy to β-cell function (4-7), the molecular signals dictating mitophagy and their significance to mitochondrial health remain largely undefined. Ubiquitination of protein substrates, catalyzed by the linkage of activated ubiquitin by three distinct enzymes (E1, E2, E3), leads to diverse responses, including substrate degradation by the ubiquitin-proteasome system, protein trafficking, complex assembly, and cellular signaling (8). Post-translational modification of downstream mitophagy effectors, including the E3 ligase Parkin, by ubiquitination is necessary for efficient mitochondrial turnover (9); however, evidence of post-translational control of proximal mitophagy regulators has not been identified. The E3 ubiquitin ligase neuregulin receptor degradation protein-1 (Nrdp1) and the deubiquitination enzyme ubiquitin specific protease-8 (USP8) counterbalance ubiquitin dynamics to direct Parkin action or its proteasomal degradation (10; 11). Nrdp1 controls Parkin-mediated mitophagy in β-cells through its interaction with, and regulation by, the diabetes gene C-type lectin domain family 16, member A (Clec16a) (4; 5); however, the precise action of Clec16a in mitophagy remains poorly understood. While these factors (Nrdp1, USP8, Clec16a) act upstream as sentinels to ensure mitophagy is utilized appropriately, the role of ubiquitination as a control mechanism for their actions is unknown. 3 Diabetes Page 4 of 46 Here we discover that formation of a ubiquitin-dependent Clec16a-Nrdp1-USP8 complex is necessary for control of mitophagy in β-cells. We identify that inhibition of Clec16a-mediated Nrdp1 ubiquitination by the chemotherapeutic agent lenalidomide impairs Clec16a-mediated mitophagy and, ultimately, reduces β-cell function. We demonstrate that Clec16a is an E3 ubiquitin ligase, which ubiquitinates Nrdp1 to promote assembly of the Clec16a-Nrdp1-USP8 mitophagy complex. Lastly, we determine that mobilization and function of the β-cell Clec16a-Nrdp1-USP8 mitophagy complex is disrupted by glucolipotoxicity. 4 Page 5 of 46 Diabetes RESEARCH DESIGN AND METHODS Patient samples- Samples were provided from de-identified non-diabetic multiple myeloma patients by the University of Michigan Hematologic Malignancies Tissue Bank and in compliance with the University of Michigan IRB. Fasting samples were collected prior to chemotherapy and again 12 weeks later. Patients received a combination of Perifosine, bortezomib, liposomal doxorubicin, Bexxar and/or carfilzomib in the presence/absence of lenalidomide (25 mg PO daily for 28 days x 4 cycles). All patients received corticosteroids (dexamethasone 40 mg PO daily x 12 doses/cycle). C-peptide and glucose concentrations were measured by chemiluminescence and the glucose oxidase method, respectively, by the University of Michigan DRC Clinical Core. Homeostatic model assessment of β-cell function and insulin resistance were calculated by HOMA2 (12). Animals- Animal studies were approved by the University of Michigan IACUC. Clec16aloxP mice (5) were mated to MIP-CreERT2 mice (13) to generate experimental groups. Recombination was induced with 3 IP injections of 150µg/g BW tamoxifen (Cayman Chemical) every other day over 5 days. 10-week old C57BL/6 mice were injected daily with 50mg/kg of lenalidomide IP or vehicle control for 3-weeks. Mice were left to recover for one week before undergoing glucose tolerance testing. Animals were housed on a standard 12-h light/12-h dark cycle with ad libitum access to food and water unless fasted prior to testing. Antibodies- A full listing of antibodies is provided in Supplementary Table 1. Proximity ligation- Studies were performed with a commercially available kit (Duolink; Sigma) per manufacturers’ protocols utilizing Nrdp1 (Bethyl Labs) and USP8 (Sigma) specific antisera. Counter staining to identify β-cells was performed in dissociated human 5 Diabetes Page 6 of 46 islets utilizing PDX-1 antisera (Santa Cruz). Proximity ligation events were quantified via ImageJ similar to published approaches (14). Imaging was performed with an IX81 microscope (Olympus). Z-stack images were captured using an ORCA Flash4 CMOS digital camera (Hamamatsu) and then subjected to deconvolution (CellSens; Olympus). Co- localization analysis was performed as previously described (5). Islet isolation and tissue culture - Primary dermal fibroblasts from WT and Ubc- CreERT;Clec16alox/lox mice were treated ex vivo with tamoxifen as previously described (5). Stably expressing Flag-Clec16a NIH3T3 cells, and Min6 cells (a gift from Dr. Doris Stoffers) were maintained as previously described (5). Mouse islets were isolated and cultured as previously described (15). Cell treatments included dimethylsulfoxide (DMSO; Fisher), lenalidomide (Ark Pharm), chloroquine (Santa Cruz Biotechnology), FCCP (Sigma), bafilomycin A1, MG132, and cycloheximide (all from EMD Millipore). Palmitate/BSA couplings were generated as previously described (16). Human islets– Studies performed on human islets procured from the Integrated Islet Distribution Program (IIDP) were approved by the University of Michigan IRB. Donor information is provided in Supplementary Table 2. Human islets were cultured in PIM(S) (Prodo Laboratories) supplemented with 10% FBS, 1% antibiotic/antimycotic (Life Technologies), and 1% PIM(G) (Prodo Laboratories). Following culture and treatments, islets were dissociated into single cells using trypsin, cytocentrifuged to glass slides, and prepared for immunostaining. Transfections- Transfection of HEK293T, HeLa, and NIH3T3 cells (Lipofectamine 2000; Life Technologies) and Min6 cells (Amaxa Nucleofector) was performed as previously 6 Page 7 of 46 Diabetes described (5). A detailed list of plasmids utilized or generated for this study is found in online supplementary material. Protein expression/purification- Recombinant Clec16a and Nrdp1 was expressed in NiCo21 (DE3) strain E.coli (NEB) following culture in auto-induction media as described (17). GST-tagged and 6xHis-tagged proteins were purified utilizing glutathione matrix or nickel-charged resin (HiCap and Ni-NTA agarose; Qiagen) per manufacturers’ protocols. In vitro transcribed/translated Clec16a and Nrdp1 were expressed in T7-driven mammalian expression systems (Promega) per manufacturers’ protocols. Clec16a and Nrdp1 protein expression/purification was confirmed by silver staining (BioRad) and/or Western blotting. Ubiquitination assays- Detection of protein ubiquitination in
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